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Sample GSM1903922 Query DataSets for GSM1903922
Status Public on Oct 10, 2015
Title Th2cell-TSA_RNA_exp2
Sample type SRA
Source name Five-day cultured Th2 cells generated from primary splenic CD4_T cells were treated with trichostatin A (TSA)
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Th2 cell
treatment: TSA
Growth protocol Splenic CD4_T cells were stimulated under Th2 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-4) for 5 days in vitro. For TSA treatment, splenic CD4 cells were cultured under Th2 conditions and 10 nM TSA (Sigma, St Louis, MO) was added in the culture on day 2 and after another 3-days of culture, Th2 cells were collected for analysis.
Extracted molecule total RNA
Extraction protocol Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
TruSeq RNA Sample Prep Kit v2 (Illumina) was used according to the manufacturer's protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description TSA-treated_Th2_cells
Data processing Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files include FPKM values for each Sample
Submission date Oct 07, 2015
Last update date May 15, 2019
Contact name Atsushi Onodera
Organization name Chiba University
Department Immunology
Street address Chuo-ku Inohana 1-8-1
City Chiba
ZIP/Postal code 260-8670
Country Japan
Platform ID GPL18480
Series (2)
GSE73813 Spatial interplay between Polycomb and Trithorax complexes controls transcriptional activity in T lymphocytes [RNA-Seq]
GSE73825 Spatial interplay between Polycomb and Trithorax complexes controls transcriptional activity in T lymphocytes
BioSample SAMN04151788
SRA SRX1310212

Supplementary file Size Download File type/resource
GSM1903922_Th2-TSA_exp2.txt.gz 251.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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